csd3
The system
1. System
2. Login
3. Directories
4. Policies
5. email
6. Languages
7. Software
8. Parallel Computing
8. ceuadmin
10. Green Algorithms
11. Training
12. Contacts
13. Acknowledgement
14. QEMU
15. A. Setup of modules
/systems/files/
Python packages
1. gwas2vcf
2. GWAS Catalog
3. ldsc
4. PhySO
5. Scikit-LLM & OpenAI API
6. snakemake
7. Synapse
R packages
1. brms
2. conquer
3. DescTools
4. EasyQC
5. geometries
6. gifski
7. glmnet
8. gnn
9. gsl
10. igraph
11. jqr
12. LDlinkR
13. magick
14. METRO
15. nloptr
16. PhenoScanner
17. PKI
18. plumber
19. protolite
20. rawrr
21. RcppTOML
22. Rfast
23. rgdal
24. rgeos
25. rgl
26. Rhdf5lib
27. rjags
28. rJava
29. RMariaDB
30. rstan
31. rtracklayer
32. SAIGE
33. sf
34. snpnet
35. sojo
36. SPACox
37. tenXplore
38. xlsx
Applications
1. ABCtoolbox
2. AEGIS
3. akt
4. ANNOVAR
5. aria2
6. bcftools
7. bedops
8. bgenix
9. CaVEMaN
10. CAVIAR/eCAVIAR
11. circos
12. citeproc
13. CookHLA
14. Cytoscape
15. DNAnexus
16. DosageConverter
17. finemap
18. GATK
19. GCTA
20. geany
21. Genotype-Harmonizer
22. gsutil
23. hail
24. HESS
25. KentUtils
26. lapack
27. LEMMA
28. LocusZoom
29. METAL
30. MetaXcan
31. pandoc
32. PCA projection
33. peer
34. pgsc_calc
35. PLINK
36. polyphen-2
37. poppler
38. PRSice
39. PRSoS
40. pspp
41. AlphaPept and PyOpenMS
42. qpdf
43. qtltools
44. quarto
45. regenie
46. R
47. RStudio
48. Rust
49. shapeit
50. SMR
51. snipar
52. SNPTEST
53. sra-tools
54. SurvivalGWAS_SV
55. tabix
56. VEP
57. Visual Studio code
58. B. Notes on emsembl-vep
/applications/files/
/applications/files/examples/
cardio
csd3
systems
policies.md
Policies
See
https://docs.hpc.cam.ac.uk/hpc/user-guide/policies.html#acknowledging-csd3
.
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2019-2024,
cambridge-ceu
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